Wyniki wyszukiwania - Biblioteka Nauki

1

Identification of specific interaction of juvenile hormone binding protein with isocitrate dehydrogenase

100%

Zalewska M. , Ożyhar A. , Kochman M.

Acta Biochimica Polonica

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2011

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tom 58

|

nr 1

119-124

EN

Juvenile hormone (JH) is essential for multiple physiological processes: it controls larval development, metamorphosis and adult reproduction. In insect hemolymph more than 99 % of JH is bound to juvenile hormone binding protein (JHBP), which protects JH from degradation by nonspecific hydrolases and serves as a carrier to supply the hormone to the target tissues. In Galleria mellonella hemolymph, JHBP is found in a complex with lipid-binding high molecular weight proteins (HMWP) and this interaction is enhanced in the presence of JH. In this report, we present studies on the interaction of JHBP with low molecular weight proteins (LMWP) in the hemolymph. Using ligand blotting we found that JHBP interacts with a protein of about 44 kDa. To identify the protein that preferentially binds JHBP, a LMWP fraction was applied to a Sepharose-bound JHBP and, after washing, the column was eluted with free JHBP acting as a specific competitor or with carbonic anhydrase as a negative control. The eluted proteins were separated by SDS/PAGE and analyzed by mass spectrometry. Isocitrate dehydrogenase was identified as a component of the supramolecular complex of JHBP with hemolymph proteins.

2

PDZ domains - common players in the cell signaling.

80%

Jeleń F. , Oleksy A. , Śmietana K. , Otlewski J.

Acta Biochimica Polonica

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2003

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tom 50

|

nr 4

985-1017

EN

PDZ domains are ubiquitous protein interaction modules that play a key role in cellular signaling. Their binding specificity involves recognition of the carboxyl-terminus of various proteins, often belonging to receptor and ion channel families. PDZ domains also mediate more complicated molecular networks through PDZ-PDZ interactions, recognition of internal protein sequences or phosphatidylinositol moieties. The domains often form a tandem of multiple copies, but equally often such tandems or single PDZ domain occur in combination with other signaling domains (for example SH3, DH/PH, GUK, LIM, CaMK). Common occurrence of PDZ domains in Metazoans strongly suggests that their evolutionary appearance results from the complication of signaling mechanisms in multicellular organisms. Here, we focus on their structure, specificity and role in signaling pathways.

3

Keram: a novel stand-alone application for correlated mutations identification and analysis

80%

Kuśka J. , Leluk J. , Lesyng B.

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2011

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tom Vol. 7, no. 1

71--76

EN

Keram is a stand-alone Windows 2000/XP/Vista application designed for the detection and analysis of the correlated mutations. Study of this phenomenon provides important information about protein structure stability factors as well as the formation of protein complexes. It is generally assumed that the mechanism of compensation explains the mutations that occur simultaneously. Keram is designed to detect the mutational correlations by comparative analysis of multiple sequence alignments. Additionally a three dimensional structure can be applied to calculate the distance between correlated positions in the protein molecule. Keram has been succesfully applied for the analysis of kinase subfamilies. The obtained data suggest that the mechanism of compensation does not explain utterly this phenomenon which seems to be much more complex and diverse. The residues that are detected as correlated are often placed at very distant positions of the protein structure, therefore the direct mutual interaction between them is impossible. We have detected not only correlated pairs, but also clusters of positions (even more than 10) that reveal correlated changeability.

4

Arginine methylation analysis of the splicing-associated SR protein SFRS9-SRP30C

80%

Bressan G. C. , Moraes E. C. , Monfiolli A. O. , Kuniyoshi T. M. , Passos D. O. , Gomes M. D. , Kobarg J.

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2009

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tom 14

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nr 4

657-669

EN

The human SFRS9/SRp30c belongs to the SR family of splicing regulators. Despite evidence that members of this protein family may be targeted by arginine methylation, this has yet to be experimentally addressed. In this study, we found that SFRS9 is a target for PRMT1-mediated arginine methylation in vitro, and that it is immunoprecipitated from HEK-293 lysates by antibodies that recognize both mono- and dimethylated arginines. We further observed that upon treatment with the methylation inhibitor Adox, the fluorescent EGFP-SFRS9 re-localizes to dot-like structures in the cell nucleus. In subsequent confocal analyses, we found that EGFP-SFRS9 localizes to nucleoli in Adox-treated cells. Our findings indicate the importance of arginine methylation for the subnuclear localization of SFRS9.

5

Application of sparse linear discriminant analysis for prediction of protein-protein interactions

80%

Stąpor K. , Fabian P.

Information Systems in Management

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2016

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tom Vol. 5, No. 1

109--118

EN

To understand the complex cellular mechanisms involved in a biological system, it is necessary to study protein-protein interactions (PPIs) at the molecular level, in which prediction of PPIs plays a significant role. In this paper we propose a new classification approach based on the sparse discriminant analysis [10] to predict obligate (permanent) and non-obligate (transient) protein-protein interactions. The sparse discriminant analysis [10] circumvents the limitations of the classical discriminant analysis [4, 9] in the high dimensional low sample size settings by incorporating inherently the feature selection into the optimization procedure. To characterize properties of protein interaction, we proposed to use the binding free energies. The performance of our proposed classifier is 75% ± 5%.

6

Human HSF1 has multiple potential targets in the preinitiation complex

80%

Yuan C. X. , Gurley W. B.

Biological Bulletin of Poznań. Supplement

|

1997

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tom 34

7

Virus-like particles of potato leafroll virus as potential carrier system for nucleic acids

80%

Suluja E. , Strokowskaja L. , Zagorski-Ostoja W. , Palucha A.

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nr 3

EN

Potato leafroll virus is a member of the polerovirus genus. The isometric virion is formed by a coat protein encapsidating single-stranded, positive-sense, mono-partite genomic RNA with covalently attached viral protein at the 5' end. The coat protein of the virus exists in two forms: i) a 23 kDa protein, the product of the coat protein gene, and ii) a 78 kDa protein, the product of the coat protein gene and an additional open reading frame expressed by read-through of the coat protein gene stop codon. The aim of this work was the expression of potato leafroll virus coat protein-based proteins that would be able to assemble into virus-like particles in insect cells. These modified particles were tested for their ability to encapsidate nucleic acids. Two types of N-terminally His-tagged coat protein constructs were used for the expression in insect cells: one, encoding a 23 kDa protein with the C-terminal amino-acid sequence corresponding to the wild type coat protein and the second with additional clathrin binding domain at the C-terminus. The expression of these two proteins by a recombinant baculovirus was characterized by Western immunoblotting with antibodies directed against potato leafroll virus. The protection or putative encapsidation of nucleic acids by these two coat protein derivatives was shown by DNase I and RNase A protection assays.

8

Identification of host proteins interacting with Toxoplasma gondii SAG1 by yeast two-hybrid assay

70%

Lai M.-Y. , Abdul-Majid N. , Lau Y.-L.

Acta Parasitologica

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2019

|

tom 64

|

nr 3

9

Interaction of maize (Zea mays) protein phosphatase 2A with tubulin

70%

Awotunde O. S. , Lechward K. , Krajewska K. , Żołnierowicz S. , Muszyńska G.

Acta Biochimica Polonica

|

2003

|

tom 50

|

nr 1

131-138

EN

Immunological and biochemical evidence has been obtained for an interaction of maize protein phosphatase 2A (PP2A) holoenzyme with tubulin. Tubulin co-purifies with maize seedling PP2A. Affinity chromatography of the maize PP2A preparation on immobilized tubulin revealed two peaks of phosphorylase a phosphatase activity. In one of the peaks, the catalytic (C) and constant regulatory (A) subunits of PP2A were identified by Western blotting. The subunits (C and A) of PP2A were co-immunoprecipitated from maize seedlings homogenate by an anti-α-tubulin antibody. The interaction of plant PP2A with tubulin indicates a possible role of reversible protein phosphorylation in the dynamic structure of plant cytoskeleton.

10

Signalling protein inhibitors via the combinatorial modification of peptide scaffolds

70%

Lawrence D. S.

Cellular and Molecular Biology Letters

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2005

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tom 10

|

nr Suppl.2

11

Methionyl-tRNA synthetase

70%

Deniziak M. A. , Barciszewski J.

Acta Biochimica Polonica

|

2001

|

tom 48

|

nr 2

EN

Methionyl-tRNA synthetase (MetRS) be longs to the fam ily of 20 en zymes es sen tial for pro tein biosynthesis. It links co va lently methionine with its cog nate tRNA. Crys tal structures solved for bac te rial MetRSs have given a num ber of in ter est ingin sights into en zyme ar chi tec ture and methionylation ca tal y sis. A com par i son of se quences of MetRSs be long ing to all king doms of life, as well as nu mer ous bio chem i cal and genetic stud ies have re vealed the pres ence of var i ous ad di tional do mains ap pended to the cat a lytic core of synthetase. They are re spon si ble for in ter ac tions with tRNA and pro teins. Ter tiary struc ture of C-terminal tRNA-binding ap pen di ces can be de duced from those de ter mined for their homo logues: tRNA bind ing pro tein 111 and en do the- lial monocyte-activating polypeptide II. Con tacts be tween MetRS and other pro teins could be me di ated not only by noncatalytic pep tides but also by struc tural el e ments pres ent in the cat a lytic core, e.g. Arg-Gly-Asp (RGD) mo tifs. Ad di tional ac tiv i ties involve MetRS in the main te nance of translational fi del ity and in co or di na tion of ri bo- some biogenesis with protein synthesis.

12

Renesans peptydów a nowe cele terapeutyczne

60%

Krzywik J. , Katarzyńska J.

Eliksir

|

2015

|

tom nr 2

15--22

13

EHDs are serine phosphoproteins: EHD1 phosphorylation is enhanced by serum stimulation

60%

Fichtman B. , Ravid L. , Rapaport D. , Horowitz M.

Cellular and Molecular Biology Letters

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2008

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tom 13

|

nr 4

632-648

EN

Endocytic processes are mediated by multiple protein-protein interacting modules and regulated by phosphorylation and dephosphorylation. The Eps15 homology domain containing protein 1 (EHD1) has been implicated in regulating recycling of proteins, internalized both in clathrin-dependent and clathrin-independent endocytic pathways, from the recycling compartment to the plasma membrane. EHD1 was found in a complex with clathrin, adaptor protein complex-2 (AP-2) and insulin-like growth factor-1 receptor (IGF-1R), and was shown to interact with Rabenosyn-5, SNAP29, EHBP1 (EH domain binding protein 1) and syndapin I and II. In this study, we show that EHD1, like the other human EHDs, undergoes serine-phosphorylation. Our results also indicate that EHD1 is a serum-inducible serine-phosphoprotein and that PKC (protein kinase C) is one of its kinases. In addition, we show that inhibitors of clathrin-mediated endocytosis decrease EHD1 phosphorylation, while inhibitors of caveolinmediated endocytosis do not affect EHD1 phosphorylation. The results of experiments in which inhibitors of endocytosis were employed strongly suggest that EHD1 phosphorylation occurs between early endosomes and the endocytic recycling compartment.

14

Architecture of the exocyst complex in plant cells

60%

Kasprowicz A. , Pihan K. , Ochocki M. , Kwiatkowski W. , Wojtaszek P.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

|

nr 3

15

WRKY transcription factors in response to ROS

60%

Vaahtera L. , Koskela M. , Jolma A. , Nurkkala H. , Varjosalo M. , Brosche M.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

|

nr 2

16

Advantage of a baculovirus expression system for protein-protein interaction studies. Involvement of posttranslational phosphorylation in the interaction between wt p53 protein and poly[ADP-ribose] polymerase-1

60%

Schmid G. , Wojciechowski J. , Wesierska-Gadek J.

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nr 3

EN

We recently observed an interaction between poly(ADP-ribose) polymerase-1 (PARP-1) and the tumor suppressor p53 protein. However, more extensive studies on both proteins, especially those on characterization of their domains involved in the interaction were difficult due to very low expression levels of p53 in mammalian cells. Therefore, we generated recombinant proteins for such studies. To clarify which domains of human PARP-1 and of human wild-type (wt) p53 were involved in this protein-protein interaction, we generated baculoviral constructs encoding full length or distinct functional domains of both proteins. Full length PARP-1 was simultaneously coexpressed in insect cells with full length wt p53 protein or its distinct truncated fragments and vice versa. Reciprocal immunoprecipitation of Sf9 cell lysates revealed that the central and carboxy-terminal fragments of p53 each were sufficient to confer binding to PARP-1, whereas the amino-terminal part harbouring the transactivation functional domain was dispensable. On the other hand, the amino-terminal and central fragments of PARP-1 were both necessary for complex formation with p53 protein. Since the most important features of p53 protein are regulated by phosphorylation, we addressed the question whether its phosphorylation is essential for the binding between the two proteins. Baculovirally expressed wt p53 was post-translationally modified. At least six distinct p53 isomers were resolved by immunoblotting following two-dimensional separation of baculovirally expressed wt p53 protein. Using specific phospho-serine antibodies, we identified phosphorylation of baculovirally expressed p53 protein at five distinct sites. To define the role of p53 phosphorylation, pull-down assays using untreated and dephosphorylated p53 protein were performed. Dephosphorylated p53 failed to bind PARP-1, indicating that complex formation between the two proteins was regulated by phosphorylation of p53. The marked phosphorylation of p53 at Ser392 observed in unstressed cells suggests that the phosphorylated carboxy-terminal part of p53 undergoes complex formation with PARP-1 resulting in masking of the NES and thereby preventing its export.

17

Protein phosphatase 2A: Variety of forms and diversity of functions

60%

Lechward K. , Awotunde O. S. , Swiatek W. , Muszynska G.

Acta Biochimica Polonica

|

2001

|

tom 48

|

nr 4

EN

Protein phosphatase 2A (PP2A) comprises a diverse family of phosphoserine- and phosphothreonine-specific phosphatases present in all eukaryotic cells. All forms of PP2A contain a catalytic subunit (PP2Ac) which forms a stable complex with thestructural subunit PR65/A. The heterodimer PP2Ac-PR65/A associates with regulatory proteins, termed variable subunits, in order to form trimeric holoenzymes attributed with distinct substrate specificity and targeted to different subcellular compartments. PP2Ac activity can be modulated by reversible phosphorylation on Tyr307 and methylation on C-terminal Leu309. Studies on PP2A have shown that this enzyme may be implicated in the regulation of metabolism, transcription, RNA splicing, translation, differentiation, cell cycle, oncogenic transformation and signal transduction.

18

Leucine-rich repeats in host-pathogen interactions

60%

Kedzierski L. , Montgomery J. , Curtis J. , Handman E.

Archivum Immunologiae et Therapiae Experimentalis

|

2004

|

tom 52

|

nr 2

19

The interactome: predicting the protein-protein interactions in cells

51%

Plewczynski D. , Ginalski K.

|

2009

|

tom 14

|

nr 1

1-22

EN

The term Interactome describes the set of all molecular interactions in cells, especially in the context of protein-protein interactions. These interactions are crucial for most cellular processes, so the full representation of the interaction repertoire is needed to understand the cell molecular machinery at the system biology level. In this short review, we compare various methods for predicting protein-protein interactions using sequence and structure information. The ultimate goal of those approaches is to present the complete methodology for the automatic selection of interaction partners using their amino acid sequences and/or three dimensional structures, if known. Apart from a description of each method, details of the software or web interface needed for high throughput prediction on the whole genome scale are also provided. The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.

20

Docking for drug interface residues of modelled VPS33B of human with PtpA of Mycobacterium tuberculosis CDC1551

51%

Reddy K. M. , Pattathil M. D. , Jayachandra S. Y. , Parameshwar A. , Sulochana M. B.

|

tom 11

|

nr 2

EN

VPS33B, a human Vacuolar Protein Sorting (VPS) protein which mediates the phagolysosomal fusion in macrophage of the eukaryotic organisms. This protein has a great role during the mycobacterial infections, which binds with the Mycobacterium protein tyrosine phosphatase A (PtpA). A single functional domain of PtpA has been identified using SMART domain databases, followed by finding the antigenicity of PtpA using CLC main workbench tool. The protein-protein interaction network predicts the interface of biological functions of proteins, built by using Cytoscape 2.8.3 version tool for manual literature survey of protein sets. According to the literature the specific interactivity of PtpA with VPS33B of human lead to pathogenesis, and provided a good platform to find the structure of VPS33B as it lacks the 3 dimensional structure in PDB. Homology Modelling of VPS33B provides a significant properties to design a specific drug through screening the drug databases (eDrug3D). The modelled protein has been validated through SAVES server maintained by NIH and UCLA with the standard Ramachandran plot with accuracy of 90.7 %. From our findings the interface residues are very crucial points which has been found through docking the modelled protein and Mycobacterium protein and interface residues were selected manually using PyMol software.